The Microarray Shared Resource (MSR) was initiated in 1999 to rapidly and cost-effectively bring the power of microarray technology to bear on cancer research. The MSR contains a fully-functional spotted microarray facility that has 3,548 ff space and prints cDNA, oligonucleotide, and protein glass slide microarrays of the highest possible quality in class 100 cleanrooms. Spotted array services include: i) availability of whole genome and targeted human and mouse spotted DNA microarrays and protocols, ii) complete project services including labeling, hybridization, scanning and primary data analysis, iii) custom array services for specialized, investigator defined, printing projects for non-standard applications, iv) complete project services for commercially available protein microarrays (e.g. Clontech Ab500) and custom printing of proteins. Investigators are able to use any or all of the tools and services offered as they require. 68 YCC members have utilized MSR spotted microarray services since its inception. This represents 22% of all Cancer Center members. During CY 2005, 19 YCC investigators accounted for 18% of the 3,550 spotted glass slide microarray provided services. The Affymetrix GeneChip section, which is included in the MSR, was established in 2001 to support large-scale gene expression studies utilizing Affymetrix oligonucleotide based microarrays. Together, the GeneChip and spotted glass slide microarray technologies offer comprehensive microarray support for cancer research which has the potential to aid in identification of biochemical causes of the disease, develop better diagnostic methods, and to improve therapeutic outcomes and patient care. The GeneChip section of the MSR occupies 1,753 ft2 of newly constructed, custom-designed laboratory space and is well equipped with GeneChip instrument systems and an ABI Sequence Detection system. Available Affymetrix services include i) expression analysis that includes RNA/mRNA extraction, preparation of target samples suitable for array hybridization, and data analysis, ii) SNP analysis using both Affymetrix (10, 100, and 500 K assays) and ABI platforms, and iii) Quantitative PCR validation of microarray results using the ABI 7900 Sequence Detection system. Both the glass slide microarray and Affymetrix GeneChip sections of the MSR will consult as needed on experimental design, data interpretation, manuscript and grant application preparation, and will provide training for labeling, hybridization and primary data analysis. During CY 2005, 25 YCC investigators using Affymetrix GeneChip services accounted for 22% of the 2,334 provided services. Since inception, the Affymetrix section has provided >6,000 services to >93 Yale investigators and 30 from other institutions.